Ginkgo Bioworks (NYSE: DNA) wins $47m DOE contract to build AI-enabled cloud lab platform

Ginkgo Bioworks Holdings Inc. (NYSE: DNA) has secured a federal contract worth up to $47 million over four years from the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory. The synthetic biology firm will design, build, and deploy a modular High-Throughput Automated Phenotyping Platform to support the Department of Energy’s Microbial Molecular Phenotyping Capability. This move aligns with broader federal efforts to upgrade America’s bioeconomy infrastructure using AI-ready cloud labs and reflects a strategic win for Ginkgo’s automation business.

The contract was awarded following a competitive procurement process under the DOE’s Office of Science, Biological and Environmental Research program. Ginkgo Bioworks was selected to co-develop an end-to-end automation system that integrates cultivation, sample preparation, and multimodal analytics, ultimately generating high-quality, reproducible microbial and microbiome data. This data is expected to power AI and machine learning models relevant to U.S. energy, climate, and biodefense priorities.

The planned platform draws heavily from Ginkgo Bioworks’ automation technologies, including its Reconfigurable Automation Carts and Catalyst scheduling software. These tools have been developed to replace static laboratory systems with flexible, cloud-enabled automation capable of adapting to evolving scientific requirements.

Why the DOE chose Ginkgo Bioworks to build its next-generation phenotyping platform

The Department of Energy’s decision to work with Ginkgo Bioworks reflects the growing policy alignment between synthetic biology and national security, energy innovation, and AI infrastructure. The platform, once deployed, will sit within the EMSL user facility operated by Pacific Northwest National Laboratory and support ongoing phenotyping campaigns across a wide variety of microbial systems.

According to the design plans released by Ginkgo Bioworks, the system will operate under biosafety level 2 compliance and support remote planning, execution, and lab integration. It is expected to provide a scalable foundation for collecting multimodal analytical measurements that can support predictive modeling in microbial science. This includes imaging, plate reading, flow cytometry, and advanced spectroscopy data collection pipelines that can be extended over time.

Ginkgo Automation General Manager Will Serber stated that the team was enthusiastic about renewing its collaboration with Pacific Northwest National Laboratory and helping expand access to high-throughput biological phenotyping. He emphasized that combining modular hardware with flexible orchestration software would give researchers the infrastructure needed to create large, AI-relevant datasets with greater efficiency and accuracy.

The decision to partner again follows previous collaborations with Pacific Northwest National Laboratory. By expanding this relationship, Ginkgo Bioworks is moving deeper into the government contracting ecosystem, particularly in the context of enabling automated science for federal research agencies.

What role does the AI-enabled cloud lab model play in Ginkgo’s growth strategy?

Ginkgo Bioworks’ contract arrives at a time when the U.S. federal government is doubling down on AI infrastructure, including biology-focused cloud labs. A recent AI Action Plan released by the Trump administration explicitly called for investment in AI-native laboratory environments that could accelerate scientific progress across climate, energy, and health.

Ginkgo Bioworks Chief Executive Officer Jason Kelly said the platform exemplifies how Ginkgo’s cloud lab capabilities are being used to build the future of scientific research infrastructure. He noted that the DOE partnership serves as a proof point for how modular lab systems, built on intelligent scheduling and automation, can drive productivity in national research labs.

The platform’s modular RAC architecture offers flexibility for new workflows or instrumentation to be added without major redesigns. Combined with Catalyst’s simulation engine, scientists can model workflows digitally to identify process bottlenecks and continuously improve throughput.

The DOE’s M2PC initiative is designed to support predictive understanding of biological systems relevant to federal missions in energy, sustainability, and biosafety. The new platform is expected to accelerate this goal by increasing data reliability, integrating AI-readiness, and allowing for continuous instrumentation upgrades.

How does the RAC and Catalyst system change scientific lab automation?

Ginkgo Bioworks’ RAC-based design enables what it refers to as function-specific “pods” that can be arranged or swapped based on evolving scientific needs. Each pod performs a defined task, such as media preparation or analytics, and is integrated with an automated transport system to move materials between workstations.

What makes this platform especially notable is its orchestration layer. Catalyst software dynamically schedules tasks across the RAC pods, allowing researchers to run multiple protocols in parallel and recover automatically from system errors. This reduces downtime and enables scale-out operations typical of cloud-native software environments, but applied to wet lab science.

Digital twin modeling, which is embedded in Catalyst, further distinguishes the platform. Researchers can simulate how new methods would perform within the existing hardware configuration, identifying delays or inefficiencies before committing resources. This simulation capability is a growing requirement for high-throughput laboratories looking to maximize utilization and reduce turnaround times.

These features make the HTP-APP a strong fit for the Department of Energy’s EMSL facility, which services hundreds of researchers across national and academic institutions. It is also a clear signal that modular, software-driven lab systems are now central to federal science funding strategies.

How is Ginkgo positioning itself for sustained growth through automation and biosecurity?

Ginkgo Bioworks has increasingly been expanding its revenue mix beyond traditional cell programming to include automation and government-focused biosecurity infrastructure. Its automation business provides integrated hardware and software platforms to research institutions, biopharma companies, and now federal agencies. Meanwhile, its biosecurity unit focuses on threat detection and biosurveillance.

This DOE contract demonstrates how Ginkgo Bioworks is aligning its offerings with U.S. science and defense goals. It also allows the company to showcase its automation stack in a real-world, federally operated laboratory environment, which could serve as a reference model for future deployments.

The synthetic biology firm’s broader strategy hinges on becoming an infrastructure layer for biology—not just a contract R&D provider. As cloud computing reshaped software delivery, Ginkgo Bioworks aims to reshape biology through programmable, scalable lab infrastructure that powers everything from strain development to AI-led biomolecular discovery.

The company’s positioning in federal bioeconomy infrastructure is becoming a differentiator at a time when investors are increasingly favoring asset-light, platform-oriented biotech firms. By participating in national lab modernization efforts, Ginkgo Bioworks is securing both revenue visibility and strategic relevance.

Ginkgo Bioworks stock gains as federal contract bolsters sentiment

Shares of Ginkgo Bioworks Holdings Inc. rose nearly 5 percent in early trading on December 5, 2025, climbing to USD 9.66 as of 10:05 am Eastern Time. The previous close was USD 9.21, and over the past five days, the stock has gained approximately 6.3 percent.

The move reflects renewed optimism surrounding the company’s federal automation pipeline and long-term strategy to monetize its synthetic biology infrastructure. Although Ginkgo Bioworks stock remains well below its 52-week high of USD 17.58, it has rebounded significantly from lows around USD 5.00 earlier in the year.

The market capitalization currently stands at approximately USD 5.5 billion, and the company is not yet reporting a price-to-earnings ratio or dividend yield, indicating it remains in a growth-focused investment phase. Institutional sentiment appears cautiously optimistic, with analysts likely to monitor whether this public-sector contract translates into additional commercial opportunities or scaled deployments.

Given the timing and strategic alignment with federal AI and scientific innovation agendas, the current investor bias appears to be a soft “Hold” with potential upside if execution continues to align with government priorities and market expansion.

Key takeaways from Ginkgo Bioworks’ $47 million DOE phenotyping platform contract

• Ginkgo Bioworks Holdings Inc. has been awarded a four-year contract worth up to $47 million by Pacific Northwest National Laboratory to build a High-Throughput Automated Phenotyping Platform (HTP-APP) for the Department of Energy’s M2PC initiative.

• The contract aims to support AI-ready microbial research by enabling automated, modular phenotyping workflows across cultivation, sample prep, and multimodal analytics including flow cytometry and mass spectrometry.

• Ginkgo’s automation platform will leverage Reconfigurable Automation Carts (RACs) and Catalyst scheduling software to allow flexible lab infrastructure, remote monitoring, digital twin simulation, and safe recovery procedures.

• The HTP-APP aligns with the Trump administration’s AI Action Plan, which calls for AI-enabled cloud labs to support national science and innovation infrastructure.

• The DOE’s M2PC program seeks to generate reproducible, high-throughput microbiome data to improve predictive modeling in biology, climate science, and biodefense.

• Ginkgo Bioworks’ automation business is gaining strategic visibility as the company pivots toward federal contracting and scientific infrastructure deployment.

• Shares of Ginkgo Bioworks (NYSE: DNA) rose nearly 5 percent to USD 9.66 on December 5, extending a 6.3 percent gain over the last five days and reflecting investor optimism around government-backed growth.

• Institutional sentiment has turned cautiously positive, with the federal contract seen as a validation of Ginkgo’s AI-native biology platform strategy.

• The company’s market cap currently stands at approximately USD 5.5 billion, with further stock momentum likely tied to execution and follow-on contract wins.